Starting phenix.real_space_refine on Sat Feb 17 10:53:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e58_27906/02_2024/8e58_27906_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e58_27906/02_2024/8e58_27906.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e58_27906/02_2024/8e58_27906_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e58_27906/02_2024/8e58_27906_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e58_27906/02_2024/8e58_27906_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e58_27906/02_2024/8e58_27906.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e58_27906/02_2024/8e58_27906.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e58_27906/02_2024/8e58_27906_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e58_27906/02_2024/8e58_27906_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians I 2 10.91 5 Ca 2 9.91 5 P 1 5.49 5 S 109 5.16 5 C 11967 2.51 5 N 2983 2.21 5 O 3385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 615": "OD1" <-> "OD2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "A PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A ASP 977": "OD1" <-> "OD2" Residue "A GLU 984": "OE1" <-> "OE2" Residue "A ASP 1180": "OD1" <-> "OD2" Residue "A ASP 1186": "OD1" <-> "OD2" Residue "A GLU 1251": "OE1" <-> "OE2" Residue "A PHE 1279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F ASP 66": "OD1" <-> "OD2" Residue "F ASP 173": "OD1" <-> "OD2" Residue "F GLU 201": "OE1" <-> "OE2" Residue "F GLU 368": "OE1" <-> "OE2" Residue "F TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 441": "OD1" <-> "OD2" Residue "F ASP 493": "OD1" <-> "OD2" Residue "F GLU 497": "OE1" <-> "OE2" Residue "F GLU 557": "OE1" <-> "OE2" Residue "F GLU 569": "OE1" <-> "OE2" Residue "F ASP 603": "OD1" <-> "OD2" Residue "F TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 657": "OE1" <-> "OE2" Residue "F ASP 668": "OD1" <-> "OD2" Residue "F ASP 677": "OD1" <-> "OD2" Residue "F PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 774": "OD1" <-> "OD2" Residue "F TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 868": "OD1" <-> "OD2" Residue "F GLU 1038": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18449 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8919 Classifications: {'peptide': 1105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 1068} Chain breaks: 9 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1326 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Chain: "F" Number of atoms: 7804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 bond proxies already assigned to first conformer: 7954 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {' CA': 1, 'BBI': 1, 'WFR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 99 Unusual residues: {' CA': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 13.38, per 1000 atoms: 0.73 Number of scatterers: 18449 At special positions: 0 Unit cell: (148.162, 138.136, 159.302, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) I 2 52.95 Ca 2 19.99 S 109 16.00 P 1 15.00 O 3385 8.00 N 2983 7.00 C 11967 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.03 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.03 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.03 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.03 Simple disulfide: pdb=" SG CYS F 670 " - pdb=" SG CYS F 700 " distance=2.03 Simple disulfide: pdb=" SG CYS F 844 " - pdb=" SG CYS F 853 " distance=2.03 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.03 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " NAG H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG B 1 " - " ASN F 350 " " NAG C 1 " - " ASN F 615 " " NAG D 1 " - " ASN F 898 " " NAG F1203 " - " ASN F 891 " " NAG F1204 " - " ASN F 92 " " NAG F1205 " - " ASN F 606 " " NAG F1206 " - " ASN F 784 " " NAG F1207 " - " ASN F1001 " " NAG F1208 " - " ASN F 988 " " NAG H 1 " - " ASN F 827 " " NAG I 1 " - " ASN F 186 " " NAG J 1 " - " ASN F 470 " Time building additional restraints: 7.98 Conformation dependent library (CDL) restraints added in 4.8 seconds 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4254 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 82 helices and 11 sheets defined 50.9% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.19 Creating SS restraints... Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 81 through 107 removed outlier: 4.129A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 142 removed outlier: 3.649A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 178 removed outlier: 3.517A pdb=" N PHE A 167 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 168 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 170 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 171 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 180 through 217 removed outlier: 3.982A pdb=" N MET A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU A 194 " --> pdb=" O PHE A 190 " (cutoff:3.500A) Proline residue: A 195 - end of helix removed outlier: 4.983A pdb=" N HIS A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE A 199 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 289 Processing helix chain 'A' and resid 294 through 305 Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'A' and resid 323 through 345 Processing helix chain 'A' and resid 434 through 451 removed outlier: 3.852A pdb=" N SER A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 485 removed outlier: 3.886A pdb=" N ARG A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 493 Processing helix chain 'A' and resid 495 through 515 removed outlier: 3.965A pdb=" N PHE A 499 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N CYS A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 540 removed outlier: 3.850A pdb=" N LEU A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 530 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ARG A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N PHE A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ILE A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 554 removed outlier: 3.876A pdb=" N SER A 551 " --> pdb=" O ASN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 581 Processing helix chain 'A' and resid 600 through 612 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 635 through 672 removed outlier: 3.660A pdb=" N CYS A 647 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A 656 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 657 " --> pdb=" O ASN A 654 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 658 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP A 662 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 817 Processing helix chain 'A' and resid 827 through 852 removed outlier: 3.887A pdb=" N LEU A 849 " --> pdb=" O VAL A 845 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A 851 " --> pdb=" O ILE A 847 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 852 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 881 Processing helix chain 'A' and resid 899 through 902 removed outlier: 3.710A pdb=" N LEU A 902 " --> pdb=" O LEU A 899 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 899 through 902' Processing helix chain 'A' and resid 904 through 910 removed outlier: 3.544A pdb=" N ASN A 909 " --> pdb=" O ARG A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 927 Processing helix chain 'A' and resid 930 through 950 Processing helix chain 'A' and resid 976 through 978 No H-bonds generated for 'chain 'A' and resid 976 through 978' Processing helix chain 'A' and resid 1000 through 1011 Processing helix chain 'A' and resid 1016 through 1024 Processing helix chain 'A' and resid 1039 through 1051 Processing helix chain 'A' and resid 1055 through 1071 removed outlier: 3.541A pdb=" N VAL A1066 " --> pdb=" O GLY A1062 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A1071 " --> pdb=" O THR A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1094 Processing helix chain 'A' and resid 1106 through 1116 removed outlier: 3.923A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1137 removed outlier: 3.518A pdb=" N MET A1137 " --> pdb=" O ILE A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1172 Processing helix chain 'A' and resid 1181 through 1205 Processing helix chain 'A' and resid 1234 through 1237 Processing helix chain 'A' and resid 1240 through 1243 removed outlier: 3.534A pdb=" N LEU A1243 " --> pdb=" O VAL A1240 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1240 through 1243' Processing helix chain 'A' and resid 1245 through 1249 Processing helix chain 'A' and resid 1251 through 1266 removed outlier: 3.605A pdb=" N PHE A1260 " --> pdb=" O LEU A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1289 removed outlier: 4.174A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A1275 " --> pdb=" O ALA A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1320 Processing helix chain 'A' and resid 1325 through 1330 Processing helix chain 'A' and resid 1355 through 1387 removed outlier: 3.504A pdb=" N TYR A1358 " --> pdb=" O ASN A1355 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A1362 " --> pdb=" O TYR A1359 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A1363 " --> pdb=" O TYR A1360 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP A1385 " --> pdb=" O ASP A1382 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A1387 " --> pdb=" O PHE A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1408 Processing helix chain 'A' and resid 1420 through 1428 removed outlier: 3.774A pdb=" N THR A1424 " --> pdb=" O ASP A1421 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 27 removed outlier: 4.008A pdb=" N THR E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 132 removed outlier: 3.610A pdb=" N PHE E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LYS E 131 " --> pdb=" O MET E 127 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 164 Proline residue: E 139 - end of helix Processing helix chain 'E' and resid 182 through 203 Processing helix chain 'F' and resid 30 through 52 Processing helix chain 'F' and resid 54 through 64 removed outlier: 3.831A pdb=" N TYR F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 110 removed outlier: 4.000A pdb=" N VAL F 79 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 97 " --> pdb=" O ARG F 93 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 137 No H-bonds generated for 'chain 'F' and resid 135 through 137' Processing helix chain 'F' and resid 179 through 201 removed outlier: 4.045A pdb=" N SER F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ALA F 190 " --> pdb=" O ASN F 186 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LEU F 191 " --> pdb=" O TRP F 187 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASP F 192 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASP F 193 " --> pdb=" O SER F 189 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 242 No H-bonds generated for 'chain 'F' and resid 240 through 242' Processing helix chain 'F' and resid 244 through 250 Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 269 through 284 removed outlier: 3.660A pdb=" N THR F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 326 removed outlier: 4.020A pdb=" N ASN F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 346 Processing helix chain 'F' and resid 372 through 378 Processing helix chain 'F' and resid 399 through 407 Processing helix chain 'F' and resid 418 through 424 removed outlier: 4.592A pdb=" N ARG F 422 " --> pdb=" O GLY F 419 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 423 " --> pdb=" O ALA F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 432 removed outlier: 3.691A pdb=" N LEU F 432 " --> pdb=" O LEU F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 443 removed outlier: 3.949A pdb=" N GLY F 440 " --> pdb=" O MET F 436 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASP F 441 " --> pdb=" O VAL F 437 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LYS F 442 " --> pdb=" O LEU F 438 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ALA F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 484 No H-bonds generated for 'chain 'F' and resid 482 through 484' Processing helix chain 'F' and resid 496 through 502 removed outlier: 3.919A pdb=" N LEU F 502 " --> pdb=" O ASP F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 545 No H-bonds generated for 'chain 'F' and resid 543 through 545' Processing helix chain 'F' and resid 563 through 566 No H-bonds generated for 'chain 'F' and resid 563 through 566' Processing helix chain 'F' and resid 571 through 581 removed outlier: 3.904A pdb=" N GLU F 575 " --> pdb=" O ASP F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 650 Processing helix chain 'F' and resid 653 through 659 removed outlier: 4.861A pdb=" N GLU F 657 " --> pdb=" O ASP F 654 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER F 659 " --> pdb=" O PHE F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 679 through 692 Processing helix chain 'F' and resid 702 through 721 Processing helix chain 'F' and resid 749 through 751 No H-bonds generated for 'chain 'F' and resid 749 through 751' Processing helix chain 'F' and resid 761 through 763 No H-bonds generated for 'chain 'F' and resid 761 through 763' Processing helix chain 'F' and resid 765 through 772 Processing helix chain 'F' and resid 821 through 829 Processing helix chain 'F' and resid 878 through 880 No H-bonds generated for 'chain 'F' and resid 878 through 880' Processing helix chain 'F' and resid 883 through 891 Processing helix chain 'F' and resid 1046 through 1049 No H-bonds generated for 'chain 'F' and resid 1046 through 1049' Processing sheet with id= A, first strand: chain 'A' and resid 225 through 228 Processing sheet with id= B, first strand: chain 'A' and resid 955 through 957 Processing sheet with id= C, first strand: chain 'A' and resid 971 through 975 Processing sheet with id= D, first strand: chain 'F' and resid 68 through 72 Processing sheet with id= E, first strand: chain 'F' and resid 167 through 169 removed outlier: 6.762A pdb=" N VAL F 468 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL F 489 " --> pdb=" O LEU F 466 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU F 466 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY F 491 " --> pdb=" O GLY F 464 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLY F 464 " --> pdb=" O GLY F 491 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP F 493 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE F 462 " --> pdb=" O ASP F 493 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 300 through 302 removed outlier: 6.084A pdb=" N ASN F 357 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU F 257 " --> pdb=" O ASN F 357 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE F 359 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU F 259 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N MET F 361 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ASP F 261 " --> pdb=" O MET F 361 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N PHE F 363 " --> pdb=" O ASP F 261 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG F 385 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU F 362 " --> pdb=" O ARG F 385 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE F 387 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N THR F 364 " --> pdb=" O PHE F 387 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N PHE F 389 " --> pdb=" O THR F 364 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR F 411 " --> pdb=" O THR F 388 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N SER F 390 " --> pdb=" O TYR F 411 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TYR F 413 " --> pdb=" O SER F 390 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 513 through 517 removed outlier: 3.511A pdb=" N THR F 592 " --> pdb=" O GLY F 605 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 661 through 664 removed outlier: 3.896A pdb=" N ILE F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS F 818 " --> pdb=" O LYS F 733 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ARG F 735 " --> pdb=" O GLY F 816 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY F 816 " --> pdb=" O ARG F 735 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N VAL F 737 " --> pdb=" O VAL F 814 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL F 814 " --> pdb=" O VAL F 737 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET F 796 " --> pdb=" O THR F 779 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 851 through 857 removed outlier: 3.661A pdb=" N MET F1020 " --> pdb=" O HIS F1007 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU F1022 " --> pdb=" O ILE F1005 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE F1005 " --> pdb=" O GLU F1022 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 895 through 902 removed outlier: 4.022A pdb=" N ILE F 978 " --> pdb=" O SER F1041 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 905 through 907 removed outlier: 3.652A pdb=" N SER F 905 " --> pdb=" O CYS F 977 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2162 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.42 Time building geometry restraints manager: 8.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 5859 1.37 - 1.52: 8874 1.52 - 1.68: 3965 1.68 - 1.83: 171 1.83 - 1.99: 2 Bond restraints: 18871 Sorted by residual: bond pdb=" C03 WFR A1903 " pdb=" C04 WFR A1903 " ideal model delta sigma weight residual 1.278 1.499 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C05 WFR A1903 " pdb=" N06 WFR A1903 " ideal model delta sigma weight residual 1.337 1.509 -0.172 2.00e-02 2.50e+03 7.39e+01 bond pdb=" C31 WFR A1903 " pdb=" C36 WFR A1903 " ideal model delta sigma weight residual 1.381 1.521 -0.140 2.00e-02 2.50e+03 4.88e+01 bond pdb=" C02 WFR A1903 " pdb=" O01 WFR A1903 " ideal model delta sigma weight residual 1.286 1.415 -0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" O18 WFR A1903 " pdb=" P19 WFR A1903 " ideal model delta sigma weight residual 1.672 1.793 -0.121 2.00e-02 2.50e+03 3.67e+01 ... (remaining 18866 not shown) Histogram of bond angle deviations from ideal: 97.94 - 114.23: 11470 114.23 - 130.51: 14064 130.51 - 146.79: 70 146.79 - 163.07: 0 163.07 - 179.35: 1 Bond angle restraints: 25605 Sorted by residual: angle pdb=" C LYS F 674 " pdb=" N PRO F 675 " pdb=" CA PRO F 675 " ideal model delta sigma weight residual 119.78 114.61 5.17 1.03e+00 9.43e-01 2.52e+01 angle pdb=" CB LYS A 894 " pdb=" CG LYS A 894 " pdb=" CD LYS A 894 " ideal model delta sigma weight residual 111.30 121.78 -10.48 2.30e+00 1.89e-01 2.08e+01 angle pdb=" CAM BBI A1902 " pdb=" CAN BBI A1902 " pdb=" CAP BBI A1902 " ideal model delta sigma weight residual 118.51 132.12 -13.61 3.00e+00 1.11e-01 2.06e+01 angle pdb=" CA LYS E 132 " pdb=" CB LYS E 132 " pdb=" CG LYS E 132 " ideal model delta sigma weight residual 114.10 121.97 -7.87 2.00e+00 2.50e-01 1.55e+01 angle pdb=" CAC BBI A1902 " pdb=" CAD BBI A1902 " pdb=" CAE BBI A1902 " ideal model delta sigma weight residual 112.57 123.85 -11.28 3.00e+00 1.11e-01 1.41e+01 ... (remaining 25600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.40: 10397 21.40 - 42.80: 902 42.80 - 64.20: 149 64.20 - 85.60: 35 85.60 - 106.99: 18 Dihedral angle restraints: 11501 sinusoidal: 4914 harmonic: 6587 Sorted by residual: dihedral pdb=" CB CYS A 245 " pdb=" SG CYS A 245 " pdb=" SG CYS A 261 " pdb=" CB CYS A 261 " ideal model delta sinusoidal sigma weight residual -86.00 -146.88 60.88 1 1.00e+01 1.00e-02 4.93e+01 dihedral pdb=" CB CYS A 226 " pdb=" SG CYS A 226 " pdb=" SG CYS A 254 " pdb=" CB CYS A 254 " ideal model delta sinusoidal sigma weight residual 93.00 46.53 46.47 1 1.00e+01 1.00e-02 2.99e+01 dihedral pdb=" CA CYS F 406 " pdb=" C CYS F 406 " pdb=" N GLU F 407 " pdb=" CA GLU F 407 " ideal model delta harmonic sigma weight residual 180.00 153.94 26.06 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 11498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.192: 2951 1.192 - 2.384: 0 2.384 - 3.576: 0 3.576 - 4.768: 0 4.768 - 5.960: 1 Chirality restraints: 2952 Sorted by residual: chirality pdb=" C04 WFR A1903 " pdb=" C03 WFR A1903 " pdb=" C05 WFR A1903 " pdb=" C10 WFR A1903 " both_signs ideal model delta sigma weight residual False 2.63 -3.33 5.96 2.00e-01 2.50e+01 8.88e+02 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN F 350 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P19 WFR A1903 " pdb=" O18 WFR A1903 " pdb=" O20 WFR A1903 " pdb=" O21 WFR A1903 " both_signs ideal model delta sigma weight residual True 3.12 -3.70 -0.58 2.00e-01 2.50e+01 8.28e+00 ... (remaining 2949 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 132 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C LYS E 132 " -0.034 2.00e-02 2.50e+03 pdb=" O LYS E 132 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG E 133 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 51 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A 52 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 846 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" CD GLU A 846 " 0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU A 846 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 846 " -0.011 2.00e-02 2.50e+03 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.75: 2730 2.75 - 3.30: 18646 3.30 - 3.86: 31298 3.86 - 4.41: 38452 4.41 - 4.96: 64647 Nonbonded interactions: 155773 Sorted by model distance: nonbonded pdb=" OG1 THR F 694 " pdb=" OD1 ASN F 696 " model vdw 2.199 2.440 nonbonded pdb=" O LEU A 849 " pdb=" OG1 THR A 852 " model vdw 2.228 2.440 nonbonded pdb=" O ALA A 838 " pdb=" OG SER A 841 " model vdw 2.240 2.440 nonbonded pdb=" OG1 THR A1259 " pdb=" OD1 ASN A1383 " model vdw 2.240 2.440 nonbonded pdb=" OG SER F 596 " pdb=" O ASP F 598 " model vdw 2.242 2.440 ... (remaining 155768 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'G' } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.910 Check model and map are aligned: 0.280 Set scattering table: 0.210 Process input model: 57.450 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.221 18871 Z= 0.431 Angle : 0.689 13.611 25605 Z= 0.337 Chirality : 0.121 5.960 2952 Planarity : 0.004 0.049 3192 Dihedral : 16.508 106.995 7208 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.43 % Favored : 94.48 % Rotamer: Outliers : 0.91 % Allowed : 13.05 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.18), residues: 2212 helix: 1.40 (0.15), residues: 1107 sheet: 0.20 (0.36), residues: 210 loop : -1.57 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 990 HIS 0.008 0.001 HIS A 992 PHE 0.018 0.002 PHE E 152 TYR 0.014 0.002 TYR F 514 ARG 0.008 0.000 ARG F 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 231 time to evaluate : 1.998 Fit side-chains revert: symmetry clash REVERT: A 500 ASP cc_start: 0.7300 (t0) cc_final: 0.7009 (t0) REVERT: A 983 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8214 (mtt) REVERT: E 53 LEU cc_start: 0.6994 (mm) cc_final: 0.6466 (mp) REVERT: F 569 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7483 (tm-30) REVERT: F 723 TRP cc_start: 0.8542 (m-10) cc_final: 0.8223 (m-10) outliers start: 18 outliers final: 7 residues processed: 241 average time/residue: 0.9982 time to fit residues: 279.9047 Evaluate side-chains 228 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 220 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 988 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 9.9990 chunk 169 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 202 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A1071 GLN E 209 GLN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.0585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18871 Z= 0.230 Angle : 0.645 31.043 25605 Z= 0.308 Chirality : 0.056 1.857 2952 Planarity : 0.005 0.045 3192 Dihedral : 8.695 90.988 2973 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.42 % Allowed : 12.80 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.18), residues: 2212 helix: 1.37 (0.15), residues: 1100 sheet: 0.35 (0.34), residues: 226 loop : -1.47 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 990 HIS 0.006 0.001 HIS A 992 PHE 0.016 0.001 PHE A1060 TYR 0.011 0.001 TYR F 514 ARG 0.005 0.000 ARG F 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 247 time to evaluate : 2.214 Fit side-chains revert: symmetry clash REVERT: A 224 LYS cc_start: 0.8527 (mttp) cc_final: 0.8163 (mtpp) REVERT: A 282 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.9027 (mmt) REVERT: A 483 MET cc_start: 0.5088 (OUTLIER) cc_final: 0.4862 (mmm) REVERT: A 894 LYS cc_start: 0.6451 (mmmt) cc_final: 0.5140 (mttp) REVERT: A 899 LEU cc_start: 0.8676 (pp) cc_final: 0.8318 (pt) REVERT: A 983 MET cc_start: 0.8775 (mtp) cc_final: 0.8487 (mtm) REVERT: A 1243 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8630 (pt) REVERT: E 53 LEU cc_start: 0.7176 (mm) cc_final: 0.6664 (mp) REVERT: E 127 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8112 (mtt) REVERT: E 165 MET cc_start: 0.4046 (OUTLIER) cc_final: 0.3590 (tpt) REVERT: F 497 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7920 (mm-30) REVERT: F 546 ARG cc_start: 0.7743 (tpp-160) cc_final: 0.6879 (tpt170) REVERT: F 603 ASP cc_start: 0.8430 (m-30) cc_final: 0.7971 (m-30) REVERT: F 858 ASP cc_start: 0.8191 (p0) cc_final: 0.7793 (p0) REVERT: F 997 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7048 (tp) REVERT: F 1038 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7791 (mt-10) outliers start: 48 outliers final: 22 residues processed: 263 average time/residue: 1.0364 time to fit residues: 315.8708 Evaluate side-chains 262 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 233 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 497 GLU Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 809 LEU Chi-restraints excluded: chain F residue 988 ASN Chi-restraints excluded: chain F residue 997 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 168 optimal weight: 0.8980 chunk 137 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 219 optimal weight: 8.9990 chunk 180 optimal weight: 0.1980 chunk 201 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 162 optimal weight: 0.1980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 909 ASN E 209 GLN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18871 Z= 0.164 Angle : 0.595 28.403 25605 Z= 0.281 Chirality : 0.057 2.074 2952 Planarity : 0.004 0.042 3192 Dihedral : 7.205 90.155 2959 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.97 % Allowed : 14.21 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.18), residues: 2212 helix: 1.39 (0.16), residues: 1104 sheet: 0.47 (0.35), residues: 226 loop : -1.38 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 187 HIS 0.003 0.001 HIS A 992 PHE 0.026 0.001 PHE A1125 TYR 0.011 0.001 TYR A 854 ARG 0.004 0.000 ARG F 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 254 time to evaluate : 1.991 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.7446 (mtm) cc_final: 0.7182 (mtp) REVERT: A 224 LYS cc_start: 0.8447 (mttp) cc_final: 0.8113 (mtpp) REVERT: A 260 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7520 (pp20) REVERT: A 482 LYS cc_start: 0.5042 (mmpt) cc_final: 0.4148 (mttm) REVERT: A 483 MET cc_start: 0.4964 (OUTLIER) cc_final: 0.4758 (mmm) REVERT: A 493 MET cc_start: 0.6455 (ptt) cc_final: 0.5312 (mtt) REVERT: A 666 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6564 (tp30) REVERT: A 669 SER cc_start: 0.6961 (OUTLIER) cc_final: 0.6568 (p) REVERT: A 894 LYS cc_start: 0.6304 (mmmt) cc_final: 0.5190 (mttp) REVERT: A 983 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8457 (mtm) REVERT: A 1243 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8496 (pt) REVERT: E 53 LEU cc_start: 0.7214 (mm) cc_final: 0.6720 (mp) REVERT: E 165 MET cc_start: 0.3868 (OUTLIER) cc_final: 0.3615 (tpt) REVERT: E 194 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7997 (mt) REVERT: F 199 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.6357 (tmm-80) REVERT: F 546 ARG cc_start: 0.7658 (tpp-160) cc_final: 0.6751 (tpt170) REVERT: F 584 GLU cc_start: 0.7599 (tt0) cc_final: 0.7383 (mt-10) REVERT: F 594 VAL cc_start: 0.9162 (t) cc_final: 0.8860 (m) REVERT: F 603 ASP cc_start: 0.8443 (m-30) cc_final: 0.8028 (m-30) REVERT: F 723 TRP cc_start: 0.8477 (m-10) cc_final: 0.8167 (m-10) REVERT: F 858 ASP cc_start: 0.8171 (p0) cc_final: 0.7682 (p0) REVERT: F 892 ILE cc_start: 0.7985 (tp) cc_final: 0.7784 (pt) REVERT: F 902 ASP cc_start: 0.8469 (t70) cc_final: 0.8218 (t0) REVERT: F 997 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.7044 (tp) REVERT: F 1018 PHE cc_start: 0.8351 (t80) cc_final: 0.8128 (t80) outliers start: 59 outliers final: 17 residues processed: 279 average time/residue: 0.9947 time to fit residues: 322.4804 Evaluate side-chains 265 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 238 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 809 LEU Chi-restraints excluded: chain F residue 988 ASN Chi-restraints excluded: chain F residue 997 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 200 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 136 optimal weight: 0.0980 chunk 203 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 192 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 209 GLN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18871 Z= 0.164 Angle : 0.594 28.494 25605 Z= 0.280 Chirality : 0.057 2.073 2952 Planarity : 0.004 0.041 3192 Dihedral : 6.689 89.174 2959 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.82 % Allowed : 15.32 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.18), residues: 2212 helix: 1.48 (0.16), residues: 1098 sheet: 0.57 (0.35), residues: 226 loop : -1.35 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 187 HIS 0.003 0.001 HIS A 992 PHE 0.025 0.001 PHE A1125 TYR 0.008 0.001 TYR A 435 ARG 0.004 0.000 ARG F 199 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 246 time to evaluate : 1.955 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.7479 (mtm) cc_final: 0.7206 (mtp) REVERT: A 224 LYS cc_start: 0.8412 (mttp) cc_final: 0.8101 (mtpp) REVERT: A 260 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: A 483 MET cc_start: 0.5028 (OUTLIER) cc_final: 0.4753 (mmp) REVERT: A 493 MET cc_start: 0.6412 (ptt) cc_final: 0.5284 (mtt) REVERT: A 666 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6555 (tp30) REVERT: A 669 SER cc_start: 0.6988 (OUTLIER) cc_final: 0.6593 (p) REVERT: A 894 LYS cc_start: 0.6336 (mmmt) cc_final: 0.5309 (mttp) REVERT: A 983 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8383 (mtt) REVERT: A 1243 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8439 (pt) REVERT: E 53 LEU cc_start: 0.7140 (mm) cc_final: 0.6727 (mp) REVERT: E 127 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8037 (mtt) REVERT: E 165 MET cc_start: 0.4065 (OUTLIER) cc_final: 0.3754 (tpt) REVERT: E 194 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7954 (mt) REVERT: F 199 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.6357 (tmm-80) REVERT: F 546 ARG cc_start: 0.7603 (tpp-160) cc_final: 0.6734 (tpt170) REVERT: F 584 GLU cc_start: 0.7633 (tt0) cc_final: 0.7411 (mt-10) REVERT: F 594 VAL cc_start: 0.9151 (t) cc_final: 0.8842 (m) REVERT: F 603 ASP cc_start: 0.8435 (m-30) cc_final: 0.8033 (m-30) REVERT: F 723 TRP cc_start: 0.8485 (m-10) cc_final: 0.8215 (m-10) REVERT: F 902 ASP cc_start: 0.8453 (t70) cc_final: 0.8157 (t0) REVERT: F 997 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7043 (tp) outliers start: 56 outliers final: 25 residues processed: 274 average time/residue: 0.9721 time to fit residues: 310.4404 Evaluate side-chains 274 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 238 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 809 LEU Chi-restraints excluded: chain F residue 988 ASN Chi-restraints excluded: chain F residue 997 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 179 optimal weight: 0.5980 chunk 122 optimal weight: 8.9990 chunk 3 optimal weight: 0.2980 chunk 160 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 193 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 ASN E 209 GLN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18871 Z= 0.223 Angle : 0.612 28.483 25605 Z= 0.289 Chirality : 0.058 2.081 2952 Planarity : 0.004 0.041 3192 Dihedral : 6.604 91.584 2959 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.53 % Allowed : 15.78 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.18), residues: 2212 helix: 1.39 (0.16), residues: 1104 sheet: 0.53 (0.35), residues: 226 loop : -1.42 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 187 HIS 0.005 0.001 HIS A 992 PHE 0.025 0.001 PHE A1125 TYR 0.010 0.001 TYR F 514 ARG 0.004 0.000 ARG F 199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 244 time to evaluate : 2.305 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.7527 (mtm) cc_final: 0.7224 (mtp) REVERT: A 224 LYS cc_start: 0.8514 (mttp) cc_final: 0.8168 (mtpp) REVERT: A 482 LYS cc_start: 0.4319 (mmpt) cc_final: 0.3396 (mttm) REVERT: A 483 MET cc_start: 0.4990 (OUTLIER) cc_final: 0.4773 (mmp) REVERT: A 493 MET cc_start: 0.6446 (ptt) cc_final: 0.5323 (mtt) REVERT: A 666 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6598 (tp30) REVERT: A 669 SER cc_start: 0.7034 (OUTLIER) cc_final: 0.6632 (p) REVERT: A 894 LYS cc_start: 0.6295 (mmmt) cc_final: 0.5284 (mttp) REVERT: A 983 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8484 (mtm) REVERT: A 1243 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8442 (pt) REVERT: A 1366 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8207 (mtm) REVERT: E 53 LEU cc_start: 0.7208 (mm) cc_final: 0.6797 (mp) REVERT: E 142 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.7310 (mpp) REVERT: E 165 MET cc_start: 0.4140 (OUTLIER) cc_final: 0.3810 (tpp) REVERT: E 194 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7907 (mt) REVERT: F 199 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.6364 (tmm-80) REVERT: F 546 ARG cc_start: 0.7655 (tpp-160) cc_final: 0.6887 (tpt170) REVERT: F 584 GLU cc_start: 0.7630 (tt0) cc_final: 0.7410 (mt-10) REVERT: F 603 ASP cc_start: 0.8420 (m-30) cc_final: 0.8036 (m-30) REVERT: F 723 TRP cc_start: 0.8505 (m-10) cc_final: 0.8239 (m-10) REVERT: F 892 ILE cc_start: 0.7937 (tp) cc_final: 0.7735 (pt) REVERT: F 902 ASP cc_start: 0.8390 (t70) cc_final: 0.8184 (t0) outliers start: 70 outliers final: 32 residues processed: 278 average time/residue: 0.9721 time to fit residues: 316.5375 Evaluate side-chains 280 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 238 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1366 MET Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 809 LEU Chi-restraints excluded: chain F residue 988 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 72 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 215 optimal weight: 8.9990 chunk 179 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 17 optimal weight: 0.0060 chunk 71 optimal weight: 0.5980 chunk 113 optimal weight: 9.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1383 ASN E 209 GLN F 108 GLN ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18871 Z= 0.142 Angle : 0.596 28.502 25605 Z= 0.278 Chirality : 0.056 2.064 2952 Planarity : 0.004 0.042 3192 Dihedral : 6.335 91.201 2959 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.82 % Allowed : 16.78 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.18), residues: 2212 helix: 1.52 (0.16), residues: 1095 sheet: 0.57 (0.35), residues: 226 loop : -1.31 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 187 HIS 0.002 0.000 HIS A 992 PHE 0.032 0.001 PHE F1006 TYR 0.008 0.001 TYR F 514 ARG 0.004 0.000 ARG F 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 242 time to evaluate : 2.172 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.7562 (mtm) cc_final: 0.7254 (mtp) REVERT: A 165 ARG cc_start: 0.7957 (mtp85) cc_final: 0.7731 (mtp-110) REVERT: A 224 LYS cc_start: 0.8412 (mttp) cc_final: 0.8126 (mtpp) REVERT: A 483 MET cc_start: 0.4908 (OUTLIER) cc_final: 0.4688 (mmp) REVERT: A 493 MET cc_start: 0.6439 (ptt) cc_final: 0.5320 (mtt) REVERT: A 669 SER cc_start: 0.7004 (OUTLIER) cc_final: 0.6598 (p) REVERT: A 894 LYS cc_start: 0.6060 (mmmt) cc_final: 0.5099 (mttp) REVERT: A 983 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8336 (mtt) REVERT: A 1243 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8330 (pt) REVERT: A 1429 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6397 (mp) REVERT: E 53 LEU cc_start: 0.7208 (mm) cc_final: 0.6839 (mp) REVERT: E 127 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8018 (mtt) REVERT: E 142 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.7300 (mpp) REVERT: E 165 MET cc_start: 0.3993 (OUTLIER) cc_final: 0.3688 (tpp) REVERT: E 194 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7923 (mt) REVERT: F 199 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.6394 (tmm-80) REVERT: F 546 ARG cc_start: 0.7626 (tpp-160) cc_final: 0.6863 (tpt170) REVERT: F 584 GLU cc_start: 0.7591 (tt0) cc_final: 0.7387 (mt-10) REVERT: F 594 VAL cc_start: 0.9120 (t) cc_final: 0.8813 (m) REVERT: F 603 ASP cc_start: 0.8387 (m-30) cc_final: 0.8011 (m-30) REVERT: F 723 TRP cc_start: 0.8493 (m-10) cc_final: 0.8207 (m-10) REVERT: F 902 ASP cc_start: 0.8335 (t70) cc_final: 0.8087 (t0) outliers start: 56 outliers final: 28 residues processed: 266 average time/residue: 1.0064 time to fit residues: 311.9401 Evaluate side-chains 274 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 236 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1429 ILE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 988 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 208 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 157 optimal weight: 0.6980 chunk 181 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 131 optimal weight: 0.0040 chunk 99 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN E 209 GLN ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18871 Z= 0.145 Angle : 0.591 28.417 25605 Z= 0.275 Chirality : 0.057 2.070 2952 Planarity : 0.004 0.042 3192 Dihedral : 6.144 91.381 2959 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.47 % Allowed : 17.44 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 2212 helix: 1.57 (0.16), residues: 1090 sheet: 0.62 (0.35), residues: 226 loop : -1.24 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 187 HIS 0.002 0.000 HIS A 992 PHE 0.024 0.001 PHE A1125 TYR 0.008 0.001 TYR A1281 ARG 0.004 0.000 ARG F 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 242 time to evaluate : 2.310 Fit side-chains REVERT: A 59 LEU cc_start: 0.7934 (mm) cc_final: 0.7509 (mt) REVERT: A 103 MET cc_start: 0.7523 (mtm) cc_final: 0.7199 (mtp) REVERT: A 165 ARG cc_start: 0.7970 (mtp85) cc_final: 0.7751 (mtp-110) REVERT: A 224 LYS cc_start: 0.8383 (mttp) cc_final: 0.8088 (mtpp) REVERT: A 493 MET cc_start: 0.6450 (ptt) cc_final: 0.5325 (mtt) REVERT: A 669 SER cc_start: 0.7020 (OUTLIER) cc_final: 0.6610 (p) REVERT: A 894 LYS cc_start: 0.5992 (mmmt) cc_final: 0.5087 (mttp) REVERT: A 983 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8339 (mtt) REVERT: A 1243 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8357 (pt) REVERT: A 1429 ILE cc_start: 0.6852 (OUTLIER) cc_final: 0.6426 (mp) REVERT: E 53 LEU cc_start: 0.7372 (mm) cc_final: 0.7000 (mp) REVERT: E 127 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8021 (mtt) REVERT: E 165 MET cc_start: 0.4045 (mpt) cc_final: 0.3733 (tpp) REVERT: E 194 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7889 (mt) REVERT: F 199 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.6518 (tmm-80) REVERT: F 546 ARG cc_start: 0.7629 (tpp-160) cc_final: 0.6870 (tpt170) REVERT: F 584 GLU cc_start: 0.7581 (tt0) cc_final: 0.7380 (mt-10) REVERT: F 594 VAL cc_start: 0.9125 (t) cc_final: 0.8823 (m) REVERT: F 603 ASP cc_start: 0.8388 (m-30) cc_final: 0.8023 (m-30) REVERT: F 723 TRP cc_start: 0.8480 (m-10) cc_final: 0.8218 (m-10) REVERT: F 892 ILE cc_start: 0.7918 (tp) cc_final: 0.7701 (pt) REVERT: F 902 ASP cc_start: 0.8297 (t70) cc_final: 0.8044 (t0) outliers start: 49 outliers final: 27 residues processed: 266 average time/residue: 0.9913 time to fit residues: 307.6599 Evaluate side-chains 268 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 234 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1429 ILE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 809 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 85 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 chunk 195 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 209 GLN ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18871 Z= 0.178 Angle : 0.615 28.450 25605 Z= 0.286 Chirality : 0.057 2.076 2952 Planarity : 0.004 0.041 3192 Dihedral : 6.124 91.814 2957 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.57 % Allowed : 17.99 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.18), residues: 2212 helix: 1.55 (0.16), residues: 1090 sheet: 0.56 (0.35), residues: 222 loop : -1.28 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 187 HIS 0.003 0.001 HIS A 992 PHE 0.030 0.001 PHE F1006 TYR 0.008 0.001 TYR F 514 ARG 0.004 0.000 ARG F 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 237 time to evaluate : 2.084 Fit side-chains REVERT: A 59 LEU cc_start: 0.7937 (mm) cc_final: 0.7513 (mt) REVERT: A 103 MET cc_start: 0.7447 (mtm) cc_final: 0.7128 (mtp) REVERT: A 165 ARG cc_start: 0.8028 (mtp85) cc_final: 0.7807 (mtp-110) REVERT: A 224 LYS cc_start: 0.8383 (mttp) cc_final: 0.8098 (mtpp) REVERT: A 493 MET cc_start: 0.6467 (ptt) cc_final: 0.5351 (mtt) REVERT: A 669 SER cc_start: 0.7010 (OUTLIER) cc_final: 0.6611 (p) REVERT: A 894 LYS cc_start: 0.6102 (mmmt) cc_final: 0.5179 (mttp) REVERT: A 983 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8464 (mtm) REVERT: A 1243 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8356 (pt) REVERT: A 1429 ILE cc_start: 0.6886 (OUTLIER) cc_final: 0.6466 (mp) REVERT: E 53 LEU cc_start: 0.7338 (mm) cc_final: 0.6936 (mm) REVERT: E 127 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8027 (mtt) REVERT: E 165 MET cc_start: 0.3948 (OUTLIER) cc_final: 0.3582 (tpp) REVERT: E 194 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7862 (mt) REVERT: F 199 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.6518 (tmm-80) REVERT: F 546 ARG cc_start: 0.7648 (tpp-160) cc_final: 0.7013 (tpt170) REVERT: F 584 GLU cc_start: 0.7579 (tt0) cc_final: 0.7361 (mt-10) REVERT: F 594 VAL cc_start: 0.9121 (t) cc_final: 0.8801 (m) REVERT: F 603 ASP cc_start: 0.8389 (m-30) cc_final: 0.8011 (m-30) REVERT: F 723 TRP cc_start: 0.8495 (m-10) cc_final: 0.8230 (m-10) REVERT: F 902 ASP cc_start: 0.8327 (t70) cc_final: 0.8073 (t0) outliers start: 51 outliers final: 31 residues processed: 265 average time/residue: 1.0048 time to fit residues: 310.8737 Evaluate side-chains 272 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 233 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1429 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 809 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 205 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 209 GLN ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18871 Z= 0.204 Angle : 0.624 28.498 25605 Z= 0.291 Chirality : 0.058 2.079 2952 Planarity : 0.004 0.041 3192 Dihedral : 6.176 92.457 2957 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.12 % Allowed : 18.85 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.18), residues: 2212 helix: 1.53 (0.16), residues: 1088 sheet: 0.52 (0.35), residues: 224 loop : -1.32 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 187 HIS 0.004 0.001 HIS A 992 PHE 0.022 0.001 PHE A1125 TYR 0.010 0.001 TYR F 514 ARG 0.005 0.000 ARG F 646 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 235 time to evaluate : 2.107 Fit side-chains REVERT: A 59 LEU cc_start: 0.7963 (mm) cc_final: 0.7561 (mt) REVERT: A 103 MET cc_start: 0.7472 (mtm) cc_final: 0.7169 (mtp) REVERT: A 165 ARG cc_start: 0.8039 (mtp85) cc_final: 0.7824 (mtp-110) REVERT: A 224 LYS cc_start: 0.8415 (mttp) cc_final: 0.8125 (mtpp) REVERT: A 482 LYS cc_start: 0.4429 (mmpt) cc_final: 0.3576 (mttm) REVERT: A 493 MET cc_start: 0.6498 (ptt) cc_final: 0.5379 (mtt) REVERT: A 669 SER cc_start: 0.6998 (OUTLIER) cc_final: 0.6599 (p) REVERT: A 846 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 894 LYS cc_start: 0.6141 (mmmt) cc_final: 0.5215 (mttp) REVERT: A 983 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8469 (mtm) REVERT: A 1243 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8379 (pt) REVERT: A 1429 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6458 (mp) REVERT: E 53 LEU cc_start: 0.7340 (mm) cc_final: 0.6934 (mm) REVERT: E 127 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8039 (mtt) REVERT: E 165 MET cc_start: 0.3836 (OUTLIER) cc_final: 0.2627 (tpp) REVERT: E 194 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7835 (mt) REVERT: F 199 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.6534 (tmm-80) REVERT: F 546 ARG cc_start: 0.7567 (tpp-160) cc_final: 0.7016 (tpt170) REVERT: F 584 GLU cc_start: 0.7648 (tt0) cc_final: 0.7372 (mt-10) REVERT: F 603 ASP cc_start: 0.8376 (m-30) cc_final: 0.8007 (m-30) REVERT: F 723 TRP cc_start: 0.8516 (m-10) cc_final: 0.8247 (m-10) REVERT: F 892 ILE cc_start: 0.8056 (tp) cc_final: 0.7802 (pt) REVERT: F 902 ASP cc_start: 0.8355 (t70) cc_final: 0.8125 (t0) outliers start: 42 outliers final: 31 residues processed: 255 average time/residue: 0.9682 time to fit residues: 288.5488 Evaluate side-chains 276 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 237 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1429 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 809 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 211 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 222 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 140 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 209 GLN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18871 Z= 0.202 Angle : 0.630 28.511 25605 Z= 0.293 Chirality : 0.058 2.078 2952 Planarity : 0.004 0.041 3192 Dihedral : 6.166 92.698 2957 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.97 % Allowed : 18.95 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.18), residues: 2212 helix: 1.52 (0.16), residues: 1086 sheet: 0.52 (0.35), residues: 224 loop : -1.36 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 187 HIS 0.004 0.001 HIS A 992 PHE 0.031 0.001 PHE F1006 TYR 0.010 0.001 TYR F 514 ARG 0.004 0.000 ARG F 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 239 time to evaluate : 2.015 Fit side-chains revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7936 (mm) cc_final: 0.7560 (mt) REVERT: A 103 MET cc_start: 0.7489 (mtm) cc_final: 0.7192 (mtp) REVERT: A 165 ARG cc_start: 0.7984 (mtp85) cc_final: 0.7783 (mtp-110) REVERT: A 224 LYS cc_start: 0.8434 (mttp) cc_final: 0.8136 (mtpp) REVERT: A 493 MET cc_start: 0.6486 (ptt) cc_final: 0.5365 (mtt) REVERT: A 500 ASP cc_start: 0.7512 (t0) cc_final: 0.7166 (t0) REVERT: A 669 SER cc_start: 0.7005 (OUTLIER) cc_final: 0.6626 (p) REVERT: A 846 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7603 (tm-30) REVERT: A 894 LYS cc_start: 0.6113 (mmmt) cc_final: 0.5185 (mttp) REVERT: A 983 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8465 (mtm) REVERT: A 1031 MET cc_start: 0.9098 (mtp) cc_final: 0.8790 (mtm) REVERT: A 1243 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8347 (pt) REVERT: A 1429 ILE cc_start: 0.6902 (OUTLIER) cc_final: 0.6486 (mp) REVERT: E 53 LEU cc_start: 0.7428 (mm) cc_final: 0.6995 (mm) REVERT: E 127 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8030 (mtt) REVERT: E 165 MET cc_start: 0.3851 (OUTLIER) cc_final: 0.2615 (tpp) REVERT: E 194 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7905 (mt) REVERT: F 199 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.6526 (tmm-80) REVERT: F 546 ARG cc_start: 0.7576 (tpp-160) cc_final: 0.7030 (tpt170) REVERT: F 584 GLU cc_start: 0.7659 (tt0) cc_final: 0.7381 (mt-10) REVERT: F 603 ASP cc_start: 0.8393 (m-30) cc_final: 0.8028 (m-30) REVERT: F 723 TRP cc_start: 0.8522 (m-10) cc_final: 0.8258 (m-10) REVERT: F 892 ILE cc_start: 0.8048 (tp) cc_final: 0.7800 (pt) REVERT: F 902 ASP cc_start: 0.8365 (t70) cc_final: 0.8151 (t0) outliers start: 39 outliers final: 31 residues processed: 258 average time/residue: 1.0450 time to fit residues: 319.5708 Evaluate side-chains 274 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 235 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1429 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 809 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 209 GLN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.158109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111576 restraints weight = 41344.167| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.94 r_work: 0.3019 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18871 Z= 0.241 Angle : 0.644 28.513 25605 Z= 0.302 Chirality : 0.058 2.082 2952 Planarity : 0.004 0.040 3192 Dihedral : 6.231 93.131 2957 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.12 % Allowed : 18.65 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.18), residues: 2212 helix: 1.47 (0.16), residues: 1088 sheet: 0.50 (0.35), residues: 224 loop : -1.38 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1112 HIS 0.005 0.001 HIS A 992 PHE 0.022 0.001 PHE A1125 TYR 0.014 0.001 TYR A1334 ARG 0.004 0.000 ARG F 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5798.67 seconds wall clock time: 104 minutes 35.44 seconds (6275.44 seconds total)